Genetic sequence data are well described by hidden Markov models (HMMs) in which latent states correspond to clusters of similar mutation patterns. Theory from statistical genetics suggests that these HMMs are nonhomogeneous (their transition probabilities vary along the chromosome) and have large support for self transitions. We develop a new nonparametric model of genetic sequence data, based on the hierarchical Dirichlet process, which supports these self transitions and nonhomogeneity. Our model provides a parameterization of the genetic process that is more parsimonious than other more general nonparametric models which have previously been applied to population genetics. We provide truncation-free MCMC inference for our model using a new auxiliary sampling scheme for Bayesian nonparametric HMMs. In a series of experiments on male X chromosome data from the Thousand Genomes Project and also on data simulated from a population bottleneck we show the benefits of our model over the popular finite model fastPHASE, which can itself be seen as a parametric truncation of our model. We find that the number of HMM states found by our model is correlated with the time to the most recent common ancestor in population bottlenecks. This work demonstrates the flexibility of Bayesian nonparametrics applied to large and complex genetic data.

Recent progress in artificial intelligence (AI) has renewed interest in building systems that learn and think like people. Many advances have come from using deep neural networks trained end-to-end in tasks such as object recognition, video games, and board games, achieving performance that equals or even beats humans in some respects. Despite their biological inspiration and performance achievements, these systems differ from human intelligence in crucial ways. We review progress in cognitive science suggesting that truly human-like learning and thinking machines will have to reach beyond current engineering trends in both what they learn, and how they learn it. Specifically, we argue that these machines should (a) build causal models of the world that support explanation and understanding, rather than merely solving pattern recognition problems; (b) ground learning in intuitive theories of physics and psychology, to support and enrich the knowledge that is learned; and (c) harness compositionality and learning-to-learn to rapidly acquire and generalize knowledge to new tasks and situations. We suggest concrete challenges and promising routes towards these goals that can combine the strengths of recent neural network advances with more structured cognitive models.

If you are a software developer who wants to learn how machine learning models work and how to apply them effectively, this book is for you. Familiarity with machine learning fundamentals and Python will be helpful, but is not essential. This book examines machine learning models including logistic regression, decision trees, and support vector machines, and applies them to common problems such as categorizing documents and classifying images. It begins with the fundamentals of machine learning, introducing you to the supervised-unsupervised spectrum, the uses of training and test data, and evaluating models. You will learn how to use generalized linear models in regression problems, as well as solve problems with text and categorical features. You will be acquainted with the use of logistic regression, regularization, and the various loss functions that are used by generalized linear models.

Model-based collaborative filtering analyzes user-item interactions to infer latent factors that represent user preferences and item characteristics in order to predict future interactions. Most collaborative filtering algorithms assume that these latent factors are static, although it has been shown that user preferences and item perceptions drift over time. In this paper, we propose a conjugate and numerically stable dynamic matrix factorization (DCPF) based on compound Poisson matrix factorization that models the smoothly drifting latent factors using Gamma-Markov chains. We propose a numerically stable Gamma chain construction, and then present a stochastic variational inference approach to estimate the parameters of our model. We apply our model to time-stamped ratings data sets: Netflix, Yelp, and Last.fm,

The analysis of nonstationary time series is of great importance in many scientific fields such as physics and neuroscience. In recent years, Gaussian process regression has attracted substantial attention as a robust and powerful method for analyzing time series. In this paper, we introduce a new framework for analyzing nonstationary time series using locally stationary Gaussian process analysis with parameters that are coupled through a hidden Markov model. The main advantage of this framework is that arbitrary complex nonstationary covariance functions can be obtained by combining simpler stationary building blocks whose hidden parameters can be estimated in closed-form. We demonstrate the flexibility of the method by analyzing two examples of synthetic nonstationary signals: oscillations with time varying frequency and time series with two dynamical states. Finally, we report an example application on real magnetoencephalographic measurements of brain activity.

Learning with sequential data is widely encountered in domains such as natural language processing, genomics, speech recognition, video processing, financial time series analysis, and so on. Recurrent neural networks (RNN) are a flexible class of sequential models which can memorize past information, and selectively pass it on across sequence steps on multiple scales. However, training RNNs is challenging in practice, and backpropagation suffers from exploding and vanishing gradients as the length of the training sequence grows. To overcome this, either RNNs are trained over short sequences or incorporate more complex architectures such as long short-term memories (LSTM). For a detailed overview of RNNs, see [20]. Figure 1 contrasts the RNN with a feedforward neural network which has no memory. On the theoretical front, understanding of RNNs is at best rudimentary. With the current techniques, it is not tractable to analyze the highly nonlinear state evolution in RNNs. Analysis of backpropagation is also intractable due to non-convexity of the loss function, and in general, reaching the global optimum is hard. Here, we take the first steps towards addressing these challenging issues.

Unavoidable dead-ends are common in many probabilistic planning problems, e.g. when actions may fail or when operating under resource constraints. An important objective in such settings is MaxProb, determining the maximal probability with which the goal can be reached, and a policy achieving that probability. Yet algorithms for MaxProb probabilistic planning are severely underexplored, to the extent that there is scant evidence of what the empirical state of the art actually is. We close this gap with a comprehensive empirical analysis. We design and explore a large space of heuristic search algorithms, systematizing known algorithms and contributing several new algorithm variants. We consider MaxProb, as well as weaker objectives that we baptize AtLeastProb (requiring to achieve a given goal probabilty threshold) and ApproxProb (requiring to compute the maximum goal probability up to a given accuracy). We explore both the general case where there may be 0-reward cycles, and the practically relevant special case of acyclic planning, such as planning with a limited action-cost budget. We design suitable termination criteria, search algorithm variants, dead-end pruning methods using classical planning heuristics, and node selection strategies. We design a benchmark suite comprising more than 1000 instances adapted from the IPPC, resource-constrained planning, and simulated penetration testing. Our evaluation clarifies the state of the art, characterizes the behavior of a wide range of heuristic search algorithms, and demonstrates significant benefits of our new algorithm variants.

Dynamical systems with large state-spaces are often expensive to thoroughly explore experimentally. Coarse-graining methods aim to define simpler systems which are more amenable to analysis and exploration; most current methods, however, focus on a priori state aggregation based on similarities in transition rates, which is not necessarily reflected in similar behaviours at the level of trajectories. We propose a way to coarsen the state-space of a system which optimally preserves the satisfaction of a set of logical specifications about the system's trajectories. Our approach is based on Gaussian Process emulation and Multi-Dimensional Scaling, a dimensionality reduction technique which optimally preserves distances in non-Euclidean spaces. We show how to obtain low-dimensional visualisations of the system's state-space from the perspective of properties' satisfaction, and how to define macro-states which behave coherently with respect to the specifications. Our approach is illustrated on a non-trivial running example, showing promising performance and high computational efficiency.

Factorial Hidden Markov Models (FHMMs) are powerful models for sequential data but they do not scale well with long sequences. We propose a scalable inference and learning algorithm for FHMMs that draws on ideas from the stochastic variational inference, neural network and copula literatures. Unlike existing approaches, the proposed algorithm requires no message passing procedure among latent variables and can be distributed to a network of computers to speed up learning. Our experiments corroborate that the proposed algorithm does not introduce further approximation bias compared to the proven structured mean-field algorithm, and achieves better performance with long sequences and large FHMMs.

We propose and study a new model for reinforcement learning with rich observations, generalizing contextual bandits to sequential decision making. These models require an agent to take actions based on observations (features) with the goal of achieving long-term performance competitive with a large set of policies. To avoid barriers to sample-efficient learning associated with large observation spaces and general POMDPs, we focus on problems that can be summarized by a small number of hidden states and have long-term rewards that are predictable by a reactive function class. In this setting, we design and analyze a new reinforcement learning algorithm, Least Squares Value Elimination by Exploration. We prove that the algorithm learns near optimal behavior after a number of episodes that is polynomial in all relevant parameters, logarithmic in the number of policies, and independent of the size of the observation space. Our result provides theoretical justification for reinforcement learning with function approximation.